1
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Wei Y, Yuan Q, Alshaya DS, Waheed A, Attia KA, Fiaz S, Iqbal MS. Characterizing the impact of CPSF30 gene disruption on TuMV infection in Arabidopsis thaliana. GM CROPS & FOOD 2024; 15:1-17. [PMID: 39351907 PMCID: PMC11445912 DOI: 10.1080/21645698.2024.2403776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 10/03/2024]
Abstract
CPSF30, a key polyadenylation factor, also serves as an m6A reader, playing a crucial role in determining RNA fate post-transcription. While its homologs mammals are known to be vital for viral replication and immune evasion, the full scope of CPSF30 in plant, particular in viral regulation, remains less explored. Our study demonstrates that CPSF30 significantly facilitates the infection of turnip mosaic virus (TuMV) in Arabidopsis thaliana, as evidenced by infection experiments on the engineered cpsf30 mutant. Among the two isoforms, CPSF30-L, which were characterized with m6A binding activity, emerged as the primary isoform responding to TuMV infection. Analysis of m6A components revealed potential involvement of the m6A machinery in regulating TuMV infection. In contrast, CPSF30-S exhibited distinct subcellular localization, coalescing with P-body markers (AtDCP1 and AtDCP2) in cytoplasmic granules, suggesting divergent regulatory mechanisms between the isoforms. Furthermore, comprehensive mRNA-Seq and miRNA-Seq analysis of Col-0 and cpsf30 mutants revealed global transcriptional reprogramming, highlighting CPSF30's role in selectively modulating gene expression during TuMV infection. In conclusion, this research underscores CPSF30's critical role in the TuMV lifecycle and sets the stage for further exploration of its function in plant viral regulation.
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Affiliation(s)
- Yanping Wei
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Quan Yuan
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Dalal Sulaiman Alshaya
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abdul Waheed
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Kotb A. Attia
- Center of Excellence in Biotechnology Research, King Saud University, Riyadh, Saudi Arabia
| | - Sajid Fiaz
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Shahid Iqbal
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
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2
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Liu S, Luo S, Yang D, Huang J, Jiang X, Yu S, Fu J, Zhou D, Chen X, He H, Fu H. Alternative polyadenylation profiles of susceptible and resistant rice (Oryza sativa L.) in response to bacterial leaf blight using RNA-seq. BMC PLANT BIOLOGY 2024; 24:145. [PMID: 38413866 PMCID: PMC10900630 DOI: 10.1186/s12870-024-04839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Alternative polyadenylation (APA) is an important pattern of post-transcriptional regulation of genes widely existing in eukaryotes, involving plant physiological and pathological processes. However, there is a dearth of studies investigating the role of APA profile in rice leaf blight. RESULTS In this study, we compared the APA profile of leaf blight-susceptible varieties (CT 9737-613P-M) and resistant varieties (NSIC RC154) following bacterial blight infection. Through gene enrichment analysis, we found that the genes of two varieties typically exhibited distal poly(A) (PA) sites that play different roles in two kinds of rice, indicating differential APA regulatory mechanisms. In this process, many disease-resistance genes displayed multiple transcripts via APA. Moreover, we also found five polyadenylation factors of similar expression patterns of rice, highlighting the critical roles of these five factors in rice response to leaf blight about PA locus diversity. CONCLUSION Notably, the present study provides the first dynamic changes of APA in rice in early response to biotic stresses and proposes a possible functional conjecture of APA in plant immune response, which lays the theoretical foundation for in-depth determination of the role of APA events in plant stress response and other life processes.
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Affiliation(s)
- Shaochun Liu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shuqi Luo
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dewei Yang
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Junying Huang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinlei Jiang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shangwei Yu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Haihui Fu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
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3
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Zhou L, Li K, Hunt AG. Natural variation in the plant polyadenylation complex. FRONTIERS IN PLANT SCIENCE 2024; 14:1303398. [PMID: 38317838 PMCID: PMC10839035 DOI: 10.3389/fpls.2023.1303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of genes in plants. Moreover, it is a point at which gene expression may be regulated by determining the functionality of the mature mRNA. Polyadenylation is mediated by a complex (the polyadenylation complex, or PAC) that consists of between 15 and 20 subunits. While the general functioning of these subunits may be inferred by extending paradigms established in well-developed eukaryotic models, much remains to be learned about the roles of individual subunits in the regulation of polyadenylation in plants. To gain further insight into this, we conducted a survey of variability in the plant PAC. For this, we drew upon a database of naturally-occurring variation in numerous geographic isolates of Arabidopsis thaliana. For a subset of genes encoding PAC subunits, the patterns of variability included the occurrence of premature stop codons in some Arabidopsis accessions. These and other observations lead us to conclude that some genes purported to encode PAC subunits in Arabidopsis are actually pseudogenes, and that others may encode proteins with dispensable functions in the plant. Many subunits of the PAC showed patterns of variability that were consistent with their roles as essential proteins in the cell. Several other PAC subunits exhibit patterns of variability consistent with selection for new or altered function. We propose that these latter subunits participate in regulatory interactions important for differential usage of poly(A) sites.
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Affiliation(s)
| | | | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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4
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Zhou J, Li QQ. Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation. MOLECULAR HORTICULTURE 2023; 3:19. [PMID: 37789388 PMCID: PMC10536700 DOI: 10.1186/s43897-023-00066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023]
Abstract
The sessile nature of plants confines their responsiveness to changing environmental conditions. Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behaviors. Alternative polyadenylation (APA) is known for its capacity to augment transcriptome diversity and plasticity, thereby furnishing an additional set of tools for modulating gene expression. APA has also been demonstrated to exhibit intimate associations with plant stress responses. In this study, we review APA dynamic features and consequences in plants subjected to both biotic and abiotic stresses. These stresses include adverse environmental stresses, and pathogenic attacks, such as cadmium toxicity, high salt, hypoxia, oxidative stress, cold, heat shock, along with bacterial, fungal, and viral infections. We analyzed the overarching research framework employed to elucidate plant APA response and the alignment of polyadenylation site transitions with the modulation of gene expression levels within the ambit of each stress condition. We also proposed a general APA model where transacting factors, including poly(A) factors, epigenetic regulators, RNA m6A modification factors, and phase separation proteins, assume pivotal roles in APA related transcriptome plasticity during stress response in plants.
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Affiliation(s)
- Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China.
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA.
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5
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Hao S, Zhang L, Zhao D, Zhou J, Ye C, Qu H, Li QQ. Inhibitor AN3661 reveals biological functions of Arabidopsis CLEAVAGE and POLYADENYLATION SPECIFICITY FACTOR 73. PLANT PHYSIOLOGY 2023; 193:537-554. [PMID: 37335917 DOI: 10.1093/plphys/kiad352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/09/2023] [Accepted: 05/21/2023] [Indexed: 06/21/2023]
Abstract
Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.
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Affiliation(s)
- Saiqi Hao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Lidan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Danhui Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Haidong Qu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
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6
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Wu Z, Liang J, Li T, Zhang D, Teng N. A LlMYB305-LlC3H18-LlWRKY33 module regulates thermotolerance in lily. MOLECULAR HORTICULTURE 2023; 3:15. [PMID: 37789438 PMCID: PMC10514960 DOI: 10.1186/s43897-023-00064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/31/2023] [Indexed: 10/05/2023]
Abstract
The CCCH proteins play important roles in plant growth and development, hormone response, pathogen defense and abiotic stress tolerance. However, the knowledge of their roles in thermotolerance are scarce. Here, we identified a heat-inducible CCCH gene LlC3H18 from lily. LlC3H18 was localized in the cytoplasm and nucleus under normal conditions, while it translocated in the cytoplasmic foci and co-located with the markers of two messenger ribonucleoprotein (mRNP) granules, processing bodies (PBs) and stress granules (SGs) under heat stress conditions, and it also exhibited RNA-binding ability. In addition, LlC3H18 exhibited transactivation activity in both yeast and plant cells. In lily and Arabidopsis, overexpression of LlC3H18 damaged their thermotolerances, and silencing of LlC3H18 in lily also impaired its thermotolerance. Similarly, Arabidopsis atc3h18 mutant also showed decreased thermotolerance. These results indicated that the appropriate expression of C3H18 was crucial for establishing thermotolerance. Further analysis found that LlC3H18 directly bound to the promoter of LlWRKY33 and activated its expression. Besides, it was found that LlMYB305 acted as an upstream factor of LlC3H18 and activated its expression. In conclusion, we demonstrated that there may be a LlMYB305-LlC3H18-LlWRKY33 regulatory module in lily that is involved in the establishment of thermotolerance and finely regulates heat stress response.
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Affiliation(s)
- Ze Wu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing, 210043, China
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahui Liang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ting Li
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing, 210043, China
| | - Dehua Zhang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing, 210043, China
| | - Nianjun Teng
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Graduate Workstation of Nanjing Agricultural University and Nanjing Oriole Island Modern Agricultural Development Co., Ltd, Nanjing, 210043, China.
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7
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Ma H, Lin J, Mei F, Mao H, Li QQ. Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:499-518. [PMID: 36786697 DOI: 10.1111/tpj.16150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 05/10/2023]
Abstract
Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co-transcriptional level. Alternative polyadenylation (APA) is an important part of co-transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37-47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress-responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time-course dynamics, and distinct 3'-UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up- and downregulated isoforms had distinct preferences for non-canonical poly(A) sites. Genes that encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal the significant role of APA in drought stress response, but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome.
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Affiliation(s)
- Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA
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8
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Ramming A, Kappel C, Kanaoka MM, Higashiyama T, Lenhard M. Poly(A) polymerase 1 contributes to competence acquisition of pollen tubes growing through the style in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:651-667. [PMID: 36811355 DOI: 10.1111/tpj.16162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/16/2023] [Indexed: 05/10/2023]
Abstract
Polyadenylation of mRNAs is critical for their export from the nucleus, stability, and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, previous studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the other two isoforms. Such functional specialization raises the possibility of an additional level of gene-expression control in plants. Here we test this notion by studying the function of PAPS1 in pollen-tube growth and guidance. Pollen tubes growing through female tissue acquire the competence to find ovules efficiently and upregulate PAPS1 expression at the transcriptional, but not detectably at the protein level compared with in vitro grown pollen tubes. Using the temperature-sensitive paps1-1 allele we show that PAPS1 activity during pollen-tube growth is required for full acquisition of competence, resulting in inefficient fertilization by paps1-1 mutant pollen tubes. While these mutant pollen tubes grow almost at the wild-type rate, they are compromised in locating the micropyles of ovules. Previously identified competence-associated genes are less expressed in paps1-1 mutant than in wild-type pollen tubes. Estimating the poly(A) tail lengths of transcripts suggests that polyadenylation by PAPS1 is associated with reduced transcript abundance. Our results therefore suggest that PAPS1 plays a key role in the acquisition of competence and underline the importance of functional specialization between PAPS isoforms throughout different developmental stages.
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Affiliation(s)
- Anna Ramming
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Christian Kappel
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Masahiro M Kanaoka
- Prefectural University of Hiroshima, Faculty of Life and Environmental Sciences, Faculty of Bioresource Sciences, Shobara, Hiroshima, Japan
| | - Tetsuya Higashiyama
- The University of Tokyo Graduate School of Science, Faculty of Science, Bunkyo-ku, Tokyo, Japan
| | - Michael Lenhard
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
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9
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de Felippes FF, Waterhouse PM. Plant terminators: the unsung heroes of gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2239-2250. [PMID: 36477559 PMCID: PMC10082929 DOI: 10.1093/jxb/erac467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/25/2022] [Indexed: 06/06/2023]
Abstract
To be properly expressed, genes need to be accompanied by a terminator, a region downstream of the coding sequence that contains the information necessary for the maturation of the mRNA 3' end. The main event in this process is the addition of a poly(A) tail at the 3' end of the new transcript, a critical step in mRNA biology that has important consequences for the expression of genes. Here, we review the mechanism leading to cleavage and polyadenylation of newly transcribed mRNAs and how this process can affect the final levels of gene expression. We give special attention to an aspect often overlooked, the effect that different terminators can have on the expression of genes. We also discuss some exciting findings connecting the choice of terminator to the biogenesis of small RNAs, which are a central part of one of the most important mechanisms of regulation of gene expression in plants.
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Affiliation(s)
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, QUT, Brisbane, QLD, Australia
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10
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Lin J, Li QQ. Coupling epigenetics and RNA polyadenylation: missing links. TRENDS IN PLANT SCIENCE 2023; 28:223-234. [PMID: 36175275 DOI: 10.1016/j.tplants.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Precise regulation of gene expression is crucial for plant survival. As a cotranscriptional regulatory mechanism, pre-mRNA polyadenylation is essential for fine-tuning gene expression. Polyadenylation can be alternatively projected at various sites of a transcript, which contributes to transcriptome diversity. Epigenetic modification is another mechanism of transcriptional control. Recent studies have uncovered crosstalk between cotranscriptional polyadenylation processes and both epigenomic and epitranscriptomic markers. Genetic analyses have demonstrated that DNA methylation, histone modifications, and epitranscriptomic modification are involved in regulating polyadenylation in plants. Here we summarize current understanding of the links between epigenetics and polyadenylation and their novel biological efficacy for plant development and environmental responses. Unresolved issues and future directions are discussed to shed light on the field.
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Affiliation(s)
- Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China; FAFU-UCR Joint Center, Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China; Biomedical Science Division, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA.
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11
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Hunt AG. Review: Mechanisms underlying alternative polyadenylation in plants - looking in the right places. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111430. [PMID: 36007628 DOI: 10.1016/j.plantsci.2022.111430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/01/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Recent years have seen an explosion of interest in the subject of alternative polyadenylation in plants. Connections between the polyadenylation complex and numerous developmental and stress responses are well-established. However, those that link stimuli with the functioning of the polyadenylation complex are less well understood. To this end, it is imperative to clearly delineate the roles of the polyadenylation complex in both plant growth AND alternative polyadenylation. It is also necessary to understand the ways by which other molecular processes may contribute to alternative polyadenylation. This review discusses these issues, with a focus on instances that reveal mechanisms by which mRNA polyadenylation may be regulated. Insights from from characterizations of mutants affected in the polyadenylation complex are discussed, as are the limitations of such characterizations when it comes to teasing out cause and effect. These limitations encourage explorations to other processes that are beyond the core polyadenylation complex. Two such processes that sculpt the plant transcriptome - transcription termination and the epigenetic control of transposon activity - also contribute to regulated poly(A) site choice. These subjects define "the right places" - molecular mechanisms that contribute to the wide-ranging control of gene expression via mRNA polyadenylation.
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Affiliation(s)
- Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, 301A Plant Science Building, 1405 Veterans Road, Lexington, KY 40546-0312, USA.
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12
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Kim JM, Ha J, Shin I, Lee JS, Park JH, Lee JD, Kang S. Identification of noble candidate gene associated with sensitivity to phytotoxicity of etofenprox in soybean. Sci Rep 2022; 12:14944. [PMID: 36056125 PMCID: PMC9440009 DOI: 10.1038/s41598-022-19323-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/26/2022] [Indexed: 11/24/2022] Open
Abstract
Phytotoxicity is caused by the interaction between plants and a chemical substance, which can cause critical damage to plants. Understanding the molecular mechanism underlying plant-chemical interactions is important for managing pests in crop fields and avoiding plant phytotoxicity by insecticides. The genomic region responsible for sensitivity to phytotoxicity of etofenprox (PE), controlled by a single dominant gene, was detected by constructing high density genetic map using recombination inbred lines (RILs) in soybean. The genomic region of ~ 80 kbp containing nine genes was identified on chromosome 16 using a high-throughput single nucleotide polymorphism (SNP) genotyping system using two different RIL populations. Through resequencing data of 31 genotypes, nonsynonymous SNPs were identified in Glyma.16g181900, Glyma.16g182200, and Glyma.16g182300. The genetic variation in Glyma.16g182200, encoding glycosylphosphatidylinositol-anchored protein (GPI-AP), caused a critical structure disruption on the active site of the protein. This structural variation of GPI-AP may change various properties of the ion channels which are the targets of pyrethroid insecticide including etofenprox. This is the first study that identifies the candidate gene and develops SNP markers associated with PE. This study would provide genomic information to understand the mechanism of phytotoxicity in soybean and functionally characterize the responsive gene.
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Affiliation(s)
- Ji-Min Kim
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, 25457, Korea
| | - Ilseob Shin
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea
| | - Ju Seok Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sungteag Kang
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, 31116, Korea.
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NBBt-test: a versatile method for differential analysis of multiple types of RNA-seq data. Sci Rep 2022; 12:12833. [PMID: 35896555 PMCID: PMC9329447 DOI: 10.1038/s41598-022-15762-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/29/2022] [Indexed: 11/25/2022] Open
Abstract
Rapid development of transcriptome sequencing technologies has resulted in a data revolution and emergence of new approaches to study transcriptomic regulation such as alternative splicing, alternative polyadenylation, CRISPR knockout screening in addition to the regular gene expression. A full characterization of the transcriptional landscape of different groups of cells or tissues holds enormous potential for both basic science as well as clinical applications. Although many methods have been developed in the realm of differential gene expression analysis, they all geared towards a particular type of sequencing data and failed to perform well when applied in different types of transcriptomic data. To fill this gap, we offer a negative beta binomial t-test (NBBt-test). NBBt-test provides multiple functions to perform differential analyses of alternative splicing, polyadenylation, CRISPR knockout screening, and gene expression datasets. Both real and large-scale simulation data show superior performance of NBBt-test with higher efficiency, and lower type I error rate and FDR to identify differential isoforms and differentially expressed genes and differential CRISPR knockout screening genes with different sample sizes when compared against the current very popular statistical methods. An R-package implementing NBBt-test is available for downloading from CRAN (https://CRAN.R-project.org/package=NBBttest).
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Wang Q, Zhuang J, Ni S, Luo H, Zheng K, Li X, Lan C, Zhao D, Bai Y, Jia B, Hu Z. Overexpressing CrePAPS Polyadenylate Activity Enhances Protein Translation and Accumulation in Chlamydomonas reinhardtii. Mar Drugs 2022; 20:276. [PMID: 35621927 PMCID: PMC9147819 DOI: 10.3390/md20050276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 02/01/2023] Open
Abstract
The alga Chlamydomonas reinhardtii is a potential platform for recombinant protein expression in the future due to various advantages. Dozens of C. reinhardtii strains producing genetically engineered recombinant therapeutic protein have been reported. However, owing to extremely low protein expression efficiency, none have been applied for industrial purposes. Improving protein expression efficiency at the molecular level is, therefore, a priority. The 3'-end poly(A) tail of mRNAs is strongly correlated with mRNA transcription and protein translation efficiency. In this study, we identified a canonical C. reinhardtii poly(A) polymerase (CrePAPS), verified its polyadenylate activity, generated a series of overexpressing transformants, and performed proteomic analysis. Proteomic results demonstrated that overexpressing CrePAPS promoted ribosomal assembly and enhanced protein accumulation. The accelerated translation was further verified by increased crude and dissolved protein content detected by Kjeldahl and bicinchoninic acid (BCA) assay approaches. The findings provide a novel direction in which to exploit photosynthetic green algae as a recombinant protein expression platform.
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Affiliation(s)
- Quan Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jieyi Zhuang
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Shuai Ni
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Haolin Luo
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Kaijie Zheng
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Xinyi Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Chengxiang Lan
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Di Zhao
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Yongsheng Bai
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
| | - Bin Jia
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518055, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (Q.W.); (J.Z.); (S.N.); (H.L.); (K.Z.); (X.L.); (C.L.); (D.Z.); (Y.B.)
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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15
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Ai Q, Pan W, Zeng Y, Li Y, Cui L. CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis. BMC PLANT BIOLOGY 2022; 22:117. [PMID: 35291942 PMCID: PMC8922935 DOI: 10.1186/s12870-022-03500-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/01/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. RESULTS In this study, a total of 53 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into eleven subfamilies according to their distinct features, and this classification was supported by intron-exon structure and conserved motif analysis. Both segmental and tandem duplication contributed to the expansion of CCCH gene family in barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The HvC3H1, HvC3H2 and HvC3H13 of arginine-rich tandem CCCH zinc finger (RR-TZF) genes were significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make them as excellent targets for the molecular breeding of barley. CONCLUSIONS Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.
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Affiliation(s)
- Qi Ai
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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16
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Zhang X, Nomoto M, Garcia-León M, Takahashi N, Kato M, Yura K, Umeda M, Rubio V, Tada Y, Furumoto T, Aoyama T, Tsuge T. CFI 25 Subunit of Cleavage Factor I is Important for Maintaining the Diversity of 3' UTR Lengths in Arabidopsis thaliana (L.) Heynh. PLANT & CELL PHYSIOLOGY 2022; 63:369-383. [PMID: 35016226 DOI: 10.1093/pcp/pcac002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Cleavage and polyadenylation at the 3' end of the pre-mRNA is essential for mRNA function, by regulating its translatability, stability and translocation to the cytoplasm. Cleavage factor I (CFI) is a multi-subunit component of the pre-mRNA 3' end processing machinery in eukaryotes. Here, we report that plant CFI 25 subunit of CFI plays an important role in maintaining the diversity of the 3' ends of mRNA. The genome of Arabidopsis thaliana (L.) Heynh. contained four genes encoding three putative CFI subunits (AtCFI 25, AtCFI 59 and AtCFI 68), orthologous to the mammalian CFI subunits. There were two CFI 25 paralogs (AtCFI 25a and AtCFI 25b) that shared homology with human CFI 25. Two null alleles of AtCFI 25a displayed smaller rosette leaves, longer stigmatic papilla, smaller anther, earlier flowering and lower fertility compared to wild-type plants. Null alleles of AtCFI 25b, as well as, plants ectopically expressing full-length cDNA of AtCFI 25a, displayed no obvious morphological defects. AtCFI 25a was shown to interact with AtCFI 25b, AtCFI 68 and itself, suggesting various forms of CFI in plants. Furthermore, we show that AtCFI 25a function was essential for maintaining proper diversity of the 3' end lengths of transcripts coding for CFI subunits, suggesting a self-regulation of the CFI machinery in plants. AtCFI 25a was also important to maintain 3' ends for other genes to different extent. Collectively, AtCFI 25a, but not AtCFI 25b, seemed to play important roles during Arabidopsis development by maintaining proper diversity of the 3' UTR lengths.
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Affiliation(s)
- Xiaojuan Zhang
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya, Aichi, 464-8601 Japan
| | - Marta Garcia-León
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan
| | - Mariko Kato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, 162-0041 Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo, 112-8610 Japan
- Center for Interdisciplinary AI and Data Science, Ochanomizu University, Bunkyo, Tokyo, 112-8610 Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan
| | - Vicente Rubio
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, Aichi, 464-8601 Japan
| | - Tsuyoshi Furumoto
- Department of Plant Life Science, Graduate School of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194 Japan
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
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17
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Ma H, Cai L, Lin J, Zhou K, Li QQ. Divergence in the Regulation of the Salt Tolerant Response Between Arabidopsis thaliana and Its Halophytic Relative Eutrema salsugineum by mRNA Alternative Polyadenylation. FRONTIERS IN PLANT SCIENCE 2022; 13:866054. [PMID: 35401636 PMCID: PMC8993227 DOI: 10.3389/fpls.2022.866054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 05/15/2023]
Abstract
Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in Arabidopsis thaliana and its halophytic relative Eutrema salsugineum with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both Arabidopsis and Eutrema, Eutrema possesses fewer APA genes than Arabidopsis (47% vs. 54%). However, the proportion of APA genes was significantly increased in Arabidopsis under salt stress but not in Eutrema. This indicated that Arabidopsis is more sensitive to salt stress and that Eutrema exhibits an innate response to such conditions. Both species utilized distal poly(A) sites under salt stress; however, only eight genes were found to overlap when their 3' untranslated region (UTR) lengthen genes were compared, thus revealing their distinct responses to salt stress. In Arabidopsis, genes that use distal poly(A) sites were enriched in response to salt stress. However, in Eutrema, the use of poly(A) sites was less affected and fewer genes were enriched. The transcripts with upregulated poly(A) sites in Arabidopsis showed enriched pathways in plant hormone signal transduction, starch and sucrose metabolism, and fatty acid elongation; in Eutrema, biosynthetic pathways (stilbenoid, diarylheptanoid, and gingerol) and metabolic pathways (arginine and proline) showed enrichment. APA was associated with 42% and 29% of the differentially expressed genes (DE genes) in Arabidopsis and Eutrema experiencing salt stress, respectively. Salt specific poly(A) sites and salt-inducible APA events were identified in both species; notably, some salt tolerance-related genes and transcription factor genes exhibited differential APA patterns, such as CIPK21 and LEA4-5. Our results suggest that adapted species exhibit more orderly response at the RNA maturation step under salt stress, while more salt-specific poly(A) sites were activated in Arabidopsis to cope with salinity conditions. Collectively, our findings not only highlight the importance of APA in the regulation of gene expression in response to salt stress, but also provide a new perspective on how salt-sensitive and salt-tolerant species perform differently under stress conditions through transcriptome diversity.
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Affiliation(s)
- Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
| | - Lingling Cai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Kaiyue Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
- *Correspondence: Qingshun Q. Li,
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18
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Architectural and functional details of CF IA proteins involved in yeast 3'-end pre-mRNA processing and its significance for eukaryotes: A concise review. Int J Biol Macromol 2021; 193:387-400. [PMID: 34699898 DOI: 10.1016/j.ijbiomac.2021.10.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 11/22/2022]
Abstract
In eukaryotes, maturation of pre-mRNA relies on its precise 3'-end processing. This processing involves co-transcriptional steps regulated by sequence elements and other proteins. Although, it holds tremendous importance, defect in the processing machinery will result in erroneous pre-mRNA maturation leading to defective translation. Remarkably, more than 20 proteins in humans and yeast share homology and execute this processing. The defects in this processing are associated with various diseases in humans. We shed light on the CF IA subunit of yeast Saccharomyces cerevisiae that contains four proteins (Pcf11, Clp1, Rna14 and Rna15) involved in this processing. Structural details of various domains of CF IA and their roles during 3'-end processing, like cleavage and polyadenylation at 3'-UTR of pre-mRNA and other cellular events are explained. Further, the chronological development and important discoveries associated with 3'-end processing are summarized. Moreover, the mammalian homologues of yeast CF IA proteins, along with their key roles are described. This knowledge would be helpful for better comprehension of the mechanism associated with this marvel; thus opening up vast avenues in this area.
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19
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Lin J, Yu Z, Ye C, Hong L, Chu Y, Shen Y, Li QQ. Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis. RNA Biol 2021; 18:2594-2604. [PMID: 34036876 PMCID: PMC8632115 DOI: 10.1080/15476286.2021.1933732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/03/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022] Open
Abstract
Alternative polyadenylation (APA) is a widespread post-transcriptional modification method that changes the 3' ends of transcripts by altering poly(A) site usage. However, the longitudinal transcriptomic 3' end profile and its mechanism of action are poorly understood. We applied diurnal time-course poly(A) tag sequencing (PAT-seq) for Arabidopsis and identified 3284 genes that generated both rhythmic and arrhythmic transcripts. These two classes of transcripts appear to exhibit dramatic differences in expression and translation activisty. The asynchronized transcripts derived by APA are embedded with different poly(A) signals, especially for rhythmic transcripts, which contain higher AAUAAA and UGUA signal proportions. The Pol II occupancy maximum is reached upstream of rhythmic poly(A) sites, while it is present directly at arrhythmic poly(A) sites. Integrating H3K9ac and H3K4me3 time-course data analyses revealed that transcriptional activation of histone markers may be involved in the differentiation of rhythmic and arrhythmic APA transcripts. These results implicate an interplay between histone modification and RNA 3'-end processing, shedding light on the mechanism of transcription rhythm and alternative polyadenylation.
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Affiliation(s)
- Juncheng Lin
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhibo Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Liwei Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yiru Chu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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20
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Ye C, Zhao D, Ye W, Wu X, Ji G, Li QQ, Lin J. QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering. Brief Bioinform 2021; 22:6319934. [PMID: 34255024 DOI: 10.1093/bib/bbab268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023] Open
Abstract
The dynamic choice of different polyadenylation sites in a gene is referred to as alternative polyadenylation, which functions in many important biological processes. Large-scale messenger RNA 3' end sequencing has revealed that cleavage sites for polyadenylation are presented with microheterogeneity. To date, the conventional determination of polyadenylation site clusters is subjective and arbitrary, leading to inaccurate annotations. Here, we present a weighted density peak clustering method, QuantifyPoly(A), to accurately quantify genome-wide polyadenylation choices. Applying QuantifyPoly(A) on published 3' end sequencing datasets from both animals and plants, their polyadenylation profiles are reshaped into myriads of novel polyadenylation site clusters. Most of these novel polyadenylation site clusters show significantly dynamic usage across different biological samples or associate with binding sites of trans-acting factors. Upstream sequences of these clusters are enriched with polyadenylation signals UGUA, UAAA and/or AAUAAA in a species-dependent manner. Polyadenylation site clusters also exhibit species specificity, while plants ones generally show higher microheterogeneity than that of animals. QuantifyPoly(A) is broadly applicable to any types of 3' end sequencing data and species for accurate quantification and construction of the complex and dynamic polyadenylation landscape and enables us to decode alternative polyadenylation events invisible to conventional methods at a much higher resolution.
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Affiliation(s)
- Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Danhui Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenbin Ye
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.,FAFU-UCR Joint Center, Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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21
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Yu H, Dai Z. SANPolyA: a deep learning method for identifying Poly(A) signals. Bioinformatics 2020; 36:2393-2400. [PMID: 31904817 DOI: 10.1093/bioinformatics/btz970] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/05/2019] [Accepted: 01/01/2020] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION Polyadenylation plays a regulatory role in transcription. The recognition of polyadenylation signal (PAS) motif sequence is an important step in polyadenylation. In the past few years, some statistical machine learning-based and deep learning-based methods have been proposed for PAS identification. Although these methods predict PAS with success, there is room for their improvement on PAS identification. RESULTS In this study, we proposed a deep neural network-based computational method, called SANPolyA, for identifying PAS in human and mouse genomes. SANPolyA requires no manually crafted sequence features. We compared our method SANPolyA with several previous PAS identification methods on several PAS benchmark datasets. Our results showed that SANPolyA outperforms the state-of-art methods. SANPolyA also showed good performance on leave-one-motif-out evaluation. AVAILABILITY AND IMPLEMENTATION https://github.com/yuht4/SANPolyA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Zhiming Dai
- School of Data and Computer Science.,Guangdong Province Key Laboratory of Big Data Analysis and Processing, Sun Yat-Sen University, Guangzhou 510006, China
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22
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Yang Y, Li Y, Sancar A, Oztas O. The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation. J Biol Chem 2020; 295:7608-7619. [PMID: 32303634 DOI: 10.1074/jbc.ra120.013513] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/10/2020] [Indexed: 01/24/2023] Open
Abstract
The circadian clock in plants temporally coordinates biological processes throughout the day, synchronizing gene expression with diurnal environmental changes. Circadian oscillator proteins are known to regulate the expression of clock-controlled plant genes by controlling their transcription. Here, using a high-throughput RNA-Seq approach, we examined genome-wide circadian and diurnal control of the Arabidopsis transcriptome, finding that the oscillation patterns of different transcripts of multitranscript genes can exhibit substantial differences and demonstrating that the circadian clock affects posttranscriptional regulation. In parallel, we found that two major posttranscriptional mechanisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA), display circadian rhythmicity resulting from oscillation in the genes involved in AS and APA. Moreover, AS-related genes exhibited rhythmic AS and APA regulation, adding another layer of complexity to circadian regulation of gene expression. We conclude that the Arabidopsis circadian clock not only controls transcription of genes but also affects their posttranscriptional regulation by influencing alternative splicing and alternative polyadenylation.
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Affiliation(s)
- Yuchen Yang
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina.,Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina.,Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Onur Oztas
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
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23
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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24
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Hunt AG. mRNA 3′ end formation in plants: Novel connections to growth, development and environmental responses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1575. [DOI: 10.1002/wrna.1575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Arthur G. Hunt
- Department of Plant and Soil Sciences University of Kentucky Lexington Kentucky
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25
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Yu Z, Lin J, Li QQ. Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation. THE PLANT CELL 2019; 31:2332-2352. [PMID: 31427469 PMCID: PMC6790095 DOI: 10.1105/tpc.18.00545] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/15/2019] [Accepted: 08/19/2019] [Indexed: 05/10/2023]
Abstract
A crucial step for mRNA polyadenylation is poly(A) signal recognition by trans-acting factors. The mammalian cleavage and polyadenylation specificity factor (CPSF) complex components CPSF30 and WD repeat-containing protein33 (WDR33) recognize the canonical AAUAAA for polyadenylation. In Arabidopsis (Arabidopsis thaliana), the flowering time regulator FY is the homolog of WDR33. However, its role in mRNA polyadenylation is poorly understood. Using poly(A) tag sequencing, we found that >50% of alternative polyadenylation (APA) events are altered in fy single mutants or double mutants with oxt6 (a null mutant of AtCPSF30), but mutation of the FY WD40-repeat has a stronger effect than deletion of the plant-unique Pro-Pro-Leu-Pro-Pro (PPLPP) domain. fy mutations disrupt AAUAAA or AAUAAA-like poly(A) signal recognition. Notably, A-rich signal usage is suppressed in the WD40-repeat mutation but promoted in PPLPP-domain deficiency. However, fy mutations do not aggravate the altered signal usage in oxt6 Furthermore, the WD40-repeat mutation shows a preference for 3' untranslated region shortening, but the PPLPP-domain deficiency shows a preference for lengthening. Interestingly, the WD40-repeat mutant exhibits shortened primary roots and late flowering with alteration of APA of related genes. Importantly, the long transcripts of two APA genes affected in fy are related to abiotic stress responses. These results reveal a conserved and specific role of FY in mRNA polyadenylation.
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Affiliation(s)
- Zhibo Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China 361102
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China 361102
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China 361102
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766
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26
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Téllez-Robledo B, Manzano C, Saez A, Navarro-Neila S, Silva-Navas J, de Lorenzo L, González-García MP, Toribio R, Hunt AG, Baigorri R, Casimiro I, Brady SM, Castellano MM, Del Pozo JC. The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1203-1219. [PMID: 31111599 DOI: 10.1111/tpj.14416] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 05/28/2023]
Abstract
Root development and its response to environmental changes is crucial for whole plant adaptation. These responses include changes in transcript levels. Here, we show that the alternative polyadenylation (APA) of mRNA is important for root development and responses. Mutations in FIP1, a component of polyadenylation machinery, affects plant development, cell division and elongation, and response to different abiotic stresses. Salt treatment increases the amount of poly(A) site usage within the coding region and 5' untranslated regions (5'-UTRs), and the lack of FIP1 activity reduces the poly(A) site usage within these non-canonical sites. Gene ontology analyses of transcripts displaying APA in response to salt show an enrichment in ABA signaling, and in the response to stresses such as salt or cadmium (Cd), among others. Root growth assays show that fip1-2 is more tolerant to salt but is hypersensitive to ABA or Cd. Our data indicate that FIP1-mediated alternative polyadenylation is important for plant development and stress responses.
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Affiliation(s)
- Barbara Téllez-Robledo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Concepcion Manzano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Angela Saez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- DTD, Timac Agro Spain, Lodosa, 31580, Navarra, Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Javier Silva-Navas
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Mary-Paz González-García
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - René Toribio
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | | | - Ilda Casimiro
- Facultad de Ciencias, Department de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - J Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
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27
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Palm D, Streit D, Shanmugam T, Weis BL, Ruprecht M, Simm S, Schleiff E. Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. Nucleic Acids Res 2019; 47:1880-1895. [PMID: 30576513 PMCID: PMC6393314 DOI: 10.1093/nar/gky1261] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 12/04/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
rRNA processing and assembly of ribosomal proteins during maturation of ribosomes involve many ribosome biogenesis factors (RBFs). Recent studies identified differences in the set of RBFs in humans and yeast, and the existence of plant-specific RBFs has been proposed as well. To identify such plant-specific RBFs, we characterized T-DNA insertion mutants of 15 Arabidopsis thaliana genes encoding nuclear proteins with nucleotide binding properties that are not orthologues to yeast or human RBFs. Mutants of nine genes show an altered rRNA processing ranging from inhibition of initial 35S pre-rRNA cleavage to final maturation events like the 6S pre-rRNA processing. These phenotypes led to their annotation as 'involved in rRNA processing' - IRP. The irp mutants are either lethal or show developmental and stress related phenotypes. We identified IRPs for maturation of the plant-specific precursor 5'-5.8S and one affecting the pathway with ITS2 first cleavage of the 35S pre-rRNA transcript. Moreover, we realized that 5'-5.8S processing is essential, while a mutant causing 6S accumulation shows only a weak phenotype. Thus, we demonstrate the importance of the maturation of the plant-specific precursor 5'-5.8S for plant development as well as the occurrence of an ITS2 first cleavage pathway in fast dividing tissues.
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Affiliation(s)
- Denise Palm
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Deniz Streit
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Thiruvenkadam Shanmugam
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Benjamin L Weis
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Maike Ruprecht
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Stefan Simm
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, D-60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, D-60438 Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, D-60438 Frankfurt, Germany
- To whom correspondence should be addressed. Tel: +49 69 798 29285; Fax: +49 69 798 29286;
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28
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Zhang Y, Ramming A, Heinke L, Altschmied L, Slotkin RK, Becker JD, Kappel C, Lenhard M. The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:655-672. [PMID: 31009115 DOI: 10.1111/tpj.14348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/21/2019] [Accepted: 04/08/2019] [Indexed: 05/28/2023]
Abstract
RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in the expression of pollen-differentiation genes, paps1 null-mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21- and particularly 24-nucleotide-long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double-mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.
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Affiliation(s)
- Yunming Zhang
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Anna Ramming
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Lisa Heinke
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Lothar Altschmied
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse 3, D-06466 Seeland, OT, Gatersleben, Germany
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
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29
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Fang X, Wang L, Ishikawa R, Li Y, Fiedler M, Liu F, Calder G, Rowan B, Weigel D, Li P, Dean C. Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes. Nature 2019; 569:265-269. [PMID: 31043738 DOI: 10.1038/s41586-019-1165-8] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/03/2019] [Indexed: 12/11/2022]
Abstract
An important component of cellular biochemistry is the concentration of proteins and nucleic acids in non-membranous compartments1,2. These biomolecular condensates are formed from processes that include liquid-liquid phase separation. The multivalent interactions necessary for liquid-liquid phase separation have been extensively studied in vitro1,3. However, the regulation of this process in vivo is poorly understood. Here we identify an in vivo regulator of liquid-liquid phase separation through a genetic screen targeting factors required for Arabidopsis RNA-binding protein FCA function. FCA contains prion-like domains that phase-separate in vitro, and exhibits behaviour in vivo that is consistent with phase separation. The mutant screen identified a functional requirement for FLL2, a coiled-coil protein, in the formation of FCA nuclear bodies. FCA reduces transcriptional read-through by promoting proximal polyadenylation at many sites in the Arabidopsis genome3,4. FLL2 was required to promote this proximal polyadenylation, but not the binding of FCA to target RNA. Ectopic expression of FLL2 increased the size and number of FCA nuclear bodies. Crosslinking with formaldehyde captured in vivo interactions between FLL2, FCA and the polymerase and nuclease modules of the RNA 3'-end processing machinery. These 3' RNA-processing components colocalized with FCA in the nuclear bodies in vivo, which indicates that FCA nuclear bodies compartmentalize 3'-end processing factors to enhance polyadenylation at specific sites. Our findings show that coiled-coil proteins can promote liquid-liquid phase separation, which expands our understanding of the principles that govern the in vivo dynamics of liquid-like bodies.
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Affiliation(s)
| | - Liang Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ryo Ishikawa
- John Innes Centre, Norwich, UK.,Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Marc Fiedler
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Fuquan Liu
- John Innes Centre, Norwich, UK.,Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | | | - Beth Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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30
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Zhou Q, Fu H, Yang D, Ye C, Zhu S, Lin J, Ye W, Ji G, Ye X, Wu X, Li QQ. Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:260-276. [PMID: 30570805 DOI: 10.1111/tpj.14209] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/26/2018] [Accepted: 12/06/2018] [Indexed: 05/25/2023]
Abstract
Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica. Using a poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage between indica and japonica, and extensive differentiation in APA profiles was detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance of indica and cold-stress tolerance of japonica. In most tissues, differential usage of APA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of the booting stage, APA site-switching genes displayed global shortening of 3' untranslated regions with increased expression in indica compared with japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis in indica than in japonica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Haihui Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Dewei Yang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Sheng Zhu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Wenbin Ye
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xinfu Ye
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, China
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31
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MacDonald CC. Tissue-specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update). WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1526. [PMID: 30816016 PMCID: PMC6617714 DOI: 10.1002/wrna.1526] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/05/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Alternative polyadenylation (APA) is how genes choose different sites for 3′ end formation for mRNAs during transcription. APA often occurs in a tissue‐ or developmental stage‐specific manner that can significantly affect gene activity by changing the protein product generated, the stability of the transcript, its localization within the cell, or its translatability. Despite the important regulatory effects that APA has on tissue‐specific gene expression, only a few examples have been characterized mechanistically. In this 2018 update to our 2010 review, we examine mechanisms for the control of APA and update our understanding of the older mechanisms since 2010. We once postulated the existence of tissue‐specific factors in APA. However, while a few tissue‐specific polyadenylation factors are known, the emerging conclusion is that the majority of APA is accomplished by altering levels of core polyadenylation proteins. Examples of those core proteins include CSTF2, CPSF1, and subunits of mammalian cleavage factor I. But despite support for these mechanisms, no one has yet documented any of these proteins changing in either a tissue‐specific or developmental manner. Given the profound effect that APA can have on gene expression and human health, improved understanding of tissue‐specific APA could lead to numerous advances in gene activity control. This article is categorized under:RNA Processing > 3′ End Processing RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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32
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Zhao Z, Wu X, Ji G, Liang C, Li QQ. Genome-Wide Comparative Analyses of Polyadenylation Signals in Eukaryotes Suggest a Possible Origin of the AAUAAA Signal. Int J Mol Sci 2019; 20:ijms20040958. [PMID: 30813258 PMCID: PMC6413133 DOI: 10.3390/ijms20040958] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 01/09/2023] Open
Abstract
Pre-mRNA cleavage and polyadenylation is an essential step for almost all mRNA in eukaryotes. The cis-elements around the poly(A) sites, however, are very diverse among different organisms. We characterized the poly(A) signals of seven different species, and compared them with that of four well-studied organisms. We found that ciliates do not show any dominant poly(A) signal; a triplet (UAA) and tetramers (UAAA and GUAA) are dominant in diatoms and red alga, respectively; and green alga Ostreococcus uses UGUAA as its poly(A) signal. Spikemoss and moss use conserved AAUAAA signals that are similar to other land plants. Our analysis suggests that the first two bases (NN in NNUAAA) are likely degenerated whereas UAAA appears to be the core motif. Combined with other published results, it is suggested that the highly conserved poly(A) signal AAUAAA may be derived from UAA with an intermediate, putative UAAA, following a pathway of UAA→UAAA→AAUAAA.
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Affiliation(s)
- Zhixin Zhao
- College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo 726000, China.
- Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen 361005, China.
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen 361005, China.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA.
| | - Qingshun Quinn Li
- Department of Biology, Miami University, Oxford, OH 45056, USA.
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, and College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA.
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de Almeida C, Scheer H, Gobert A, Fileccia V, Martinelli F, Zuber H, Gagliardi D. RNA uridylation and decay in plants. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0163. [PMID: 30397100 DOI: 10.1098/rstb.2018.0163] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2018] [Indexed: 12/13/2022] Open
Abstract
RNA uridylation consists of the untemplated addition of uridines at the 3' extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algae Chlamydomonas reinhardtii and the flowering plant Arabidopsis thaliana Plant TUTases target a variety of RNA substrates, differing in size and function. These RNA substrates include microRNAs (miRNAs), small interfering silencing RNAs (siRNAs), ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) and mRNA fragments generated during post-transcriptional gene silencing. Viral RNAs can also get uridylated during plant infection. We describe here the evolutionary history of plant TUTases and we summarize the diverse molecular functions of uridylation during RNA degradation processes in plants. We also outline key points of future research.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Caroline de Almeida
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Hélène Scheer
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Veronica Fileccia
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università degli Studi di Palermo, viale delle scienze ed. 4, Palermo 90128, Italy
| | - Federico Martinelli
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università degli Studi di Palermo, viale delle scienze ed. 4, Palermo 90128, Italy
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes (IBMP), Centre national de la recherche scientifique (CNRS), Université de Strasbourg, 12 rue Zimmer, 67000 Strasbourg, France
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Characterization of mRNA polyadenylation in the apicomplexa. PLoS One 2018; 13:e0203317. [PMID: 30161237 PMCID: PMC6117058 DOI: 10.1371/journal.pone.0203317] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/18/2018] [Indexed: 11/19/2022] Open
Abstract
Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15–20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two—poly(A) polymerase and CPSF73—of the 19 proteins used as queries in this analysis. As the human subunits that recognize the AAUAAA polyadenylation signal (PAS) were not immediately obvious, a computational analysis of sequences adjacent to experimentally-determined apicomplexan poly(A) sites was conducted. The results of this study showed that there exists in apicomplexans an A-rich region that corresponds in position to the AAUAAA PAS. The set of experimentally-determined sites in one species, Sarcocystis neurona, was further analyzed to evaluate the extent and significance of alternative poly(A) site choice in this organism. The results showed that almost 80% of S. neurona genes possess more than one poly(A) site, and that more than 780 sites showed differential usage in the two developmental stages–extracellular merozoites and intracellular schizonts–studied. These sites affected more than 450 genes, and included a disproportionate number of genes that encode membrane transporters and ribosomal proteins. Taken together, these results reveal that apicomplexan species seem to possess a poly(A) signal analogous to AAUAAA even though genes that may encode obvious counterparts of the AAUAAA-recognizing proteins are absent in these organisms. They also indicate that, as is the case in other eukaryotes, alternative polyadenylation is a widespread phenomenon in S. neurona that has the potential to impact growth and development.
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Genome-wide atlas of alternative polyadenylation in the forage legume red clover. Sci Rep 2018; 8:11379. [PMID: 30054540 PMCID: PMC6063945 DOI: 10.1038/s41598-018-29699-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
Studies on prevalence and significance of alternative polyadenylation (APA) in plants have been so far limited mostly to the model plants. Here, a genome-wide analysis of APA was carried out in different tissue types in the non-model forage legume red clover (Trifolium pratense L). A profile of poly(A) sites in different tissue types was generated using so-called 'poly(A)-tag sequencing' (PATseq) approach. Our analysis revealed tissue-wise dynamics of usage of poly(A) sites located at different genomic locations. We also identified poly(A) sites and underlying genes displaying APA in different tissues. Functional categories enriched in groups of genes manifesting APA between tissue types were determined. Analysis of spatial expression of genes encoding different poly(A) factors showed significant differential expression of genes encoding orthologs of FIP1(V) and PCFS4, suggesting that these two factors may play a role in regulating spatial APA in red clover. Our analysis also revealed a high degree of conservation in diverse plant species of APA events in mRNAs encoding two key polyadenylation factors, CPSF30 and FIP1(V). Together with our previously reported study of spatial gene expression in red clover, this study will provide a comprehensive account of transcriptome dynamics in this non-model forage legume.
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Molecular Regulation of Nitrate Responses in Plants. Int J Mol Sci 2018; 19:ijms19072039. [PMID: 30011829 PMCID: PMC6073361 DOI: 10.3390/ijms19072039] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022] Open
Abstract
Nitrogen is an essential macronutrient that affects plant growth and development. Improving the nitrogen use efficiency of crops is of great importance for the economic and environmental sustainability of agriculture. Nitrate (NO3−) is a major form of nitrogen absorbed by most crops and also serves as a vital signaling molecule. Research has identified key molecular components in nitrate signaling mainly by employing forward and reverse genetics as well as systems biology. In this review, we focus on advances in the characterization of genes involved in primary nitrate responses as well as the long-term effects of nitrate, especially in terms of how nitrate regulates root development.
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Lai Y, Eulgem T. Transcript-level expression control of plant NLR genes. MOLECULAR PLANT PATHOLOGY 2018; 19:1267-1281. [PMID: 28834153 PMCID: PMC6638128 DOI: 10.1111/mpp.12607] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 05/20/2023]
Abstract
Plant NLR genes encode sensitive immune receptors that can mediate the specific recognition of pathogen avirulence effectors and activate a strong defence response, termed effector-triggered immunity. The expression of NLRs requires strict regulation, as their ability to trigger immunity is dependent on their dose, and overexpression of NLRs results in autoimmunity and massive fitness costs. An elaborate interplay of different mechanisms controlling NLR transcript levels allows plants to maximize their defence capacity, whilst limiting negative impact on their fitness. Global suppression of NLR transcripts may be a prerequisite for the fast evolution of new NLR variants and the expansion of this gene family. Here, we summarize recent progress made towards a comprehensive understanding of NLR transcript-level expression control. Multiple mechanistic steps, including transcription as well as co-/post-transcriptional processing and transcript turn-over, contribute to balanced base levels of NLR transcripts and allow for dynamic adjustments to defence situations.
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Affiliation(s)
- Yan Lai
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
- College of Life SciencesFujian Agricultural and Forestry UniversityFuzhouFujian 350002China
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
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Seok HY, Nguyen LV, Park HY, Tarte VN, Ha J, Lee SY, Moon YH. Arabidopsis non-TZF gene AtC3H17 functions as a positive regulator in salt stress response. Biochem Biophys Res Commun 2018; 498:954-959. [PMID: 29548822 DOI: 10.1016/j.bbrc.2018.03.088] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 11/24/2022]
Abstract
Functional studies of CCCH-type zinc finger proteins in abiotic stress responses have largely focused on tandem CCCH-type zinc finger (TZF) genes, whereas the study of functional roles of non-TZF genes in abiotic stress responses has largely been neglected. Here, we investigated the functional roles of AtC3H17, a non-TZF gene of Arabidopsis, in salt stress responses. AtC3H17 expression significantly increased under NaCl, mannitol, and ABA treatments. AtC3H17-overexpressing transgenic plants (OXs) were more tolerant under NaCl and MV treatment conditions than the wild type (WT). atc3h17 mutants were more sensitive under NaCl and MV treatment conditions compared with the WT. The transcription of the salt stress-responsive genes in ABA-dependent pathway, such as RAB18, COR15A, and RD22, was significantly higher in AtC3H17 OXs than in WT both under NaCl-free condition and after NaCl treatment. Our results demonstrate that AtC3H17 functions as a positive regulator in salt stress response, via the up-regulation of ABA-dependent salt stress-response pathway.
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Affiliation(s)
- Hye-Yeon Seok
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Linh Vu Nguyen
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Hee-Yeon Park
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Vaishali N Tarte
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Jimin Ha
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Sun-Young Lee
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Yong-Hwan Moon
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea.
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Vandereyken K, Van Leene J, De Coninck B, Cammue BPA. Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. FRONTIERS IN PLANT SCIENCE 2018; 9:694. [PMID: 29922309 PMCID: PMC5996676 DOI: 10.3389/fpls.2018.00694] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/07/2018] [Indexed: 05/20/2023]
Abstract
Plant stress responses involve numerous changes at the molecular and cellular level and are regulated by highly complex signaling pathways. Studying protein-protein interactions (PPIs) and the resulting networks is therefore becoming increasingly important in understanding these responses. Crucial in PPI networks are the so-called hubs or hub proteins, commonly defined as the most highly connected central proteins in scale-free PPI networks. However, despite their importance, a growing amount of confusion and controversy seems to exist regarding hub protein identification, characterization and classification. In order to highlight these inconsistencies and stimulate further clarification, this review critically analyses the current knowledge on hub proteins in the plant interactome field. We focus on current hub protein definitions, including the properties generally seen as hub-defining, and the challenges and approaches associated with hub protein identification. Furthermore, we give an overview of the most important large-scale plant PPI studies of the last decade that identified hub proteins, pointing out the lack of overlap between different studies. As such, it appears that although major advances are being made in the plant interactome field, defining hub proteins is still heavily dependent on the quality, origin and interpretation of the acquired PPI data. Nevertheless, many hub proteins seem to have a reported role in the plant stress response, including transcription factors, protein kinases and phosphatases, ubiquitin proteasome system related proteins, (co-)chaperones and redox signaling proteins. A significant number of identified plant stress hubs are however still functionally uncharacterized, making them interesting targets for future research. This review clearly shows the ongoing improvements in the plant interactome field but also calls attention to the need for a more comprehensive and precise identification of hub proteins, allowing a more efficient systems biology driven unraveling of complex processes, including those involved in stress responses.
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Affiliation(s)
- Katy Vandereyken
- Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jelle Van Leene
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Barbara De Coninck
- Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
| | - Bruno P. A. Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- *Correspondence: Bruno P. A. Cammue
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Wang C, Zhang W, Li Z, Li Z, Bi Y, Crawford NM, Wang Y. FIP1 Plays an Important Role in Nitrate Signaling and Regulates CIPK8 and CIPK23 Expression in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:593. [PMID: 29780398 PMCID: PMC5945890 DOI: 10.3389/fpls.2018.00593] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/16/2018] [Indexed: 05/20/2023]
Abstract
Unraveling the molecular mechanisms of nitrate regulation and deciphering the underlying genetic network is vital for elucidating nitrate uptake and utilization in plants. Such knowledge could lead to the improvement of nitrogen-use efficiency in agriculture. Here, we report that the FIP1 gene (factor interacting with poly(A) polymerase 1) plays an important role in nitrate signaling in Arabidopsis thaliana. FIP1 encodes a putative core component of the polyadenylation factor complex. We found that FIP1 interacts with the cleavage and polyadenylation specificity factor 30-L (CPSF30-L), which is also an essential player in nitrate signaling. The induction of nitrate-responsive genes following nitrate treatment was inhibited in the fip1 mutant. The nitrate content was also reduced in fip1 seedlings due to their decreased nitrate uptake activity. Furthermore, the nitrate content was higher in the roots but lower in the roots of fip1, which may result from the downregulation of NRT1.8 and the upregulation of the nitrate assimilation genes. In addition, qPCR analyses revealed that FIP1 negatively regulated the expression of CIPK8 and CIPK23, two protein kinases involved in nitrate signaling. In the fip1 mutant, the increased expression of CIPK23 may affect nitrate uptake, resulting in its lower nitrate content. Genetic and molecular evidence suggests that FIP1 and CPSF30-L function in the same nitrate-signaling pathway, with FIP1 mediating signaling through its interaction with CPSF30-L and its regulation of CIPK8 and CIPK23. Analysis of the 3'-UTR of NRT1.1 showed that the pattern of polyadenylation sites was altered in the fip1 mutant. These findings add a novel component to the nitrate regulation network and enhance our understanding of the underlying mechanisms for nitrate signaling.
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Affiliation(s)
- Chao Wang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- Section of General Biology, Department of Life Science and Engineering, Jining University, Jining, China
| | - Wenjing Zhang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Zehui Li
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Zhen Li
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Yingjun Bi
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Nigel M. Crawford
- Section of Cell and Developmental Biology, Division of Biological Science, University of California at San Diego, La Jolla, CA, United States
| | - Yong Wang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yong Wang,
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Hong L, Ye C, Lin J, Fu H, Wu X, Li QQ. Alternative polyadenylation is involved in auxin-based plant growth and development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:246-258. [PMID: 29155478 DOI: 10.1111/tpj.13771] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 10/24/2017] [Accepted: 10/31/2017] [Indexed: 05/24/2023]
Abstract
Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, the effect of auxin on pre-mRNA post-transcriptional regulation is mostly unknown. By using a poly(A) tag (PAT) sequencing approach, mRNA alternative polyadenylation (APA) profiles after auxin treatment were revealed. We showed that hundreds of poly(A) site clusters (PACs) are affected by auxin at the transcriptome level, where auxin reduces PAC distribution in 5'-untranslated region (UTR), but increases in the 3'UTR. APA site usage frequencies of 42 genes were switched by auxin, suggesting that auxin affects the choice of poly(A) sites. Furthermore, poly(A) signal selection was altered after auxin treatment. For example, a mutant of poly(A) signal binding protein CPSF30 showed altered sensitivity to auxin treatment, indicating interactions between auxin and the poly(A) signal recognition machinery. We also found that auxin activity on lateral root development is likely mediated by altered expression of ARF7, ARF19 and IAA14 through poly(A) site switches. Our results shed light on the molecular mechanisms of auxin responses relative to its interactions with mRNA polyadenylation.
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Affiliation(s)
- Liwei Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Haihui Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
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Lin J, Xu R, Wu X, Shen Y, Li QQ. Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:829-839. [PMID: 28621907 DOI: 10.1111/tpj.13611] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/17/2017] [Accepted: 05/22/2017] [Indexed: 05/28/2023]
Abstract
CPSF100 is a core component of the cleavage and polyadenylation specificity factor (CPSF) complex for 3'-end formation of mRNA, but it still has no clear functional assignment. CPSF100 was reported to play a role in RNA silencing and promote flowering in Arabidopsis. However, the molecular mechanisms underlying these phenomena are not fully understood. Our genetics analyses indicate that plants with a hypomorphic mutant of CPSF100 (esp5) show defects in embryogenesis, reduced seed production or altered root morphology. To unravel this puzzle, we employed a poly(A) tag sequencing protocol and uncovered a different poly(A) profile in esp5. This transcriptome-wide analysis revealed alternative polyadenylation of thousands of genes, most of which result in transcriptional read-through in protein-coding genes. AtCPSF100 also affects poly(A) signal recognition on the far-upstream elements; in particular it prefers less U-rich sequences. Importantly, AtCPSF100 was found to exert its functions through the change of poly(A) sites on genes encoding binding proteins, such as nucleotide-binding, RNA-binding and poly(U)-binding proteins. In addition, through its interaction with RNA Polymerase II C-terminal domain (CTD) and affecting the expression level of CTD phosphatase-like 3 (CPL3), AtCPSF100 is shown to potentially ensure transcriptional termination by dephosphorylation of Ser2 on the CTD. These data suggest a key role for CPSF100 in locating poly(A) sites and affecting transcription termination.
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Affiliation(s)
- Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Ruqiang Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
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Shan P, Fan G, Sun L, Liu J, Wang W, Hu C, Zhang X, Zhai Q, Song X, Cao L, Cui Y, Zhang S, Wang C. SIRT1 Functions as a Negative Regulator of Eukaryotic Poly(A)RNA Transport. Curr Biol 2017; 27:2271-2284.e5. [PMID: 28756945 DOI: 10.1016/j.cub.2017.06.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 05/04/2017] [Accepted: 06/15/2017] [Indexed: 10/19/2022]
Abstract
Most eukaryotic mRNAs are polyadenylated in the nucleus, and the poly(A)-tail is required for efficient mRNA export and translation. However, mechanisms governing mRNA transport remain unclear. Here, we report that the nicotinamide adenine dinucleotide (NAD)-dependent deacetylase SIRT1 acts as an energy sensor and negatively regulates poly(A)RNA transport via deacetylating a poly(A)-binding protein, PABP1. Upon energy starvation, SIRT1 interacts with and deacetylates PABP1 and deactivates its poly(A)RNA binding, leading to nuclear accumulation of PABP1 and poly(A)RNA and thus facilitating eukaryotic cells to attenuate protein synthesis and energy consumption to adapt to energy stress. Moreover, AMPK-directed SIRT1 phosphorylation is required for energy starvation-induced PABP1-SIRT1 association, PABP1 deacetylation, and poly(A)RNA nuclear retention. In addition, the SIRT1-PABP1 association is not specific to energy starvation but represents a common stress response. These observations provide insights into dynamic modulation of eukaryotic mRNA transport and translation, suggesting that the poly(A)-tail also provides a basis for eukaryotes to effectively shut down mature mRNA transport and thereby tailor protein synthesis to maintain energy homeostasis under stress conditions.
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Affiliation(s)
- Peipei Shan
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Guangjian Fan
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Lianhui Sun
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Jinqin Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai 200241, China
| | - Weifang Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai 200241, China
| | - Chen Hu
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, Detroit, MI 48201, USA
| | - Xiaohong Zhang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, Detroit, MI 48201, USA
| | - Qiwei Zhai
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoyu Song
- Key Laboratory of Medical Cell Biology, College of Translational Medicine, China Medical University, Shengyang 110000, China
| | - Liu Cao
- Key Laboratory of Medical Cell Biology, College of Translational Medicine, China Medical University, Shengyang 110000, China
| | - Yongping Cui
- Key Laboratory of Cellular Physiology Ministry of Education, Shanxi Medical University, Shanxi 030001, China
| | - Shengping Zhang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China.
| | - Chuangui Wang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China; Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China; Shanghai Key Laboratory of Fundus Diseases, 100 Haining Road, Shanghai 200080, China.
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Interplay between Alternative Splicing and Alternative Polyadenylation Defines the Expression Outcome of the Plant Unique OXIDATIVE TOLERANT-6 Gene. Sci Rep 2017; 7:2052. [PMID: 28515442 PMCID: PMC5435732 DOI: 10.1038/s41598-017-02215-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/06/2017] [Indexed: 11/16/2022] Open
Abstract
Pre-mRNA alternative splicing and alternative polyadenylation have been implicated to play important roles during eukaryotic gene expression. However, much remains unknown regarding the regulatory mechanisms and the interactions of these two processes in plants. Here we focus on an Arabidopsis gene OXT6 (Oxidative Tolerant-6) that has been demonstrated to encode two proteins through alternative splicing and alternative polyadenylation. Specifically, alternative polyadenylation at Intron-2 of OXT6 produces a transcript coding for AtCPSF30, an Arabidopsis ortholog of 30 kDa subunit of the Cleavage and Polyadenylation Specificity Factor. On the other hand, alternative splicing of Intron-2 generates a longer transcript encoding a protein named AtC30Y, a polypeptide including most part of AtCPSF30 and a YT521B domain. To investigate the expression outcome of OXT6 in plants, a set of mutations were constructed to alter the splicing and polyadenylation patterns of OXT6. Analysis of transgenic plants bearing these mutations by quantitative RT-PCR revealed a competition relationship between these two processes. Moreover, when both splice sites and poly(A) signals were mutated, polyadenylation became the preferred mode of OXT6 processing. These results demonstrate the interplay between alternative splicing and alternative polyadenylation, and it is their concerted actions that define a gene’s expression outcome.
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Antosz W, Pfab A, Ehrnsberger HF, Holzinger P, Köllen K, Mortensen SA, Bruckmann A, Schubert T, Längst G, Griesenbeck J, Schubert V, Grasser M, Grasser KD. The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors. THE PLANT CELL 2017; 29:854-870. [PMID: 28351991 PMCID: PMC5435424 DOI: 10.1105/tpc.16.00735] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/22/2017] [Accepted: 03/26/2017] [Indexed: 05/03/2023]
Abstract
Transcript elongation factors (TEFs) are a heterogeneous group of proteins that control the efficiency of transcript elongation of subsets of genes by RNA polymerase II (RNAPII) in the chromatin context. Using reciprocal tagging in combination with affinity purification and mass spectrometry, we demonstrate that in Arabidopsis thaliana, the TEFs SPT4/SPT5, SPT6, FACT, PAF1-C, and TFIIS copurified with each other and with elongating RNAPII, while P-TEFb was not among the interactors. Additionally, NAP1 histone chaperones, ATP-dependent chromatin remodeling factors, and some histone-modifying enzymes including Elongator were repeatedly found associated with TEFs. Analysis of double mutant plants defective in different combinations of TEFs revealed genetic interactions between genes encoding subunits of PAF1-C, FACT, and TFIIS, resulting in synergistic/epistatic effects on plant growth/development. Analysis of subnuclear localization, gene expression, and chromatin association did not provide evidence for an involvement of the TEFs in transcription by RNAPI (or RNAPIII). Proteomics analyses also revealed multiple interactions between the transcript elongation complex and factors involved in mRNA splicing and polyadenylation, including an association of PAF1-C with the polyadenylation factor CstF. Therefore, the RNAPII transcript elongation complex represents a platform for interactions among different TEFs, as well as for coordinating ongoing transcription with mRNA processing.
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Affiliation(s)
- Wojciech Antosz
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Alexander Pfab
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Hans F Ehrnsberger
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Philipp Holzinger
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Karin Köllen
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Simon A Mortensen
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Schubert
- Department for Biochemistry III, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Gernot Längst
- Department for Biochemistry III, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Department for Biochemistry III, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt Seeland, Germany
| | - Marion Grasser
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg, D-93053 Regensburg, Germany
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Jensen GS, Fal K, Hamant O, Haswell ES. The RNA Polymerase-Associated Factor 1 Complex Is Required for Plant Touch Responses. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:499-511. [PMID: 28204553 PMCID: PMC5441907 DOI: 10.1093/jxb/erw439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Thigmomorphogenesis is a stereotypical developmental alteration in the plant body plan that can be induced by repeatedly touching plant organs. To unravel how plants sense and record multiple touch stimuli we performed a novel forward genetic screen based on the development of a shorter stem in response to repetitive touch. The touch insensitive (ths1) mutant identified in this screen is defective in some aspects of shoot and root thigmomorphogenesis. The ths1 mutant is an intermediate loss-of-function allele of VERNALIZATION INDEPENDENCE 3 (VIP3), a previously characterized gene whose product is part of the RNA polymerase II-associated factor 1 (Paf1) complex. The Paf1 complex is found in yeast, plants and animals, and has been implicated in histone modification and RNA processing. Several components of the Paf1 complex are required for reduced stem height in response to touch and normal root slanting and coiling responses. Global levels of histone H3K36 trimethylation are reduced in VIP3 mutants. In addition, THS1/VIP3 is required for wild type histone H3K36 trimethylation at the TOUCH3 (TCH3) and TOUCH4 (TCH4) loci and for rapid touch-induced upregulation of TCH3 and TCH4 transcripts. Thus, an evolutionarily conserved chromatin-modifying complex is required for both short- and long-term responses to mechanical stimulation, providing insight into how plants record mechanical signals for thigmomorphogenesis.
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Affiliation(s)
- Gregory S Jensen
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Kateryna Fal
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Olivier Hamant
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Elizabeth S Haswell
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, USA
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Fu H, Yang D, Su W, Ma L, Shen Y, Ji G, Ye X, Wu X, Li QQ. Genome-wide dynamics of alternative polyadenylation in rice. Genome Res 2016; 26:1753-1760. [PMID: 27733415 PMCID: PMC5131826 DOI: 10.1101/gr.210757.116] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/06/2016] [Indexed: 12/02/2022]
Abstract
Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3'-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3' UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3'-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes.
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Affiliation(s)
- Haihui Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, 361102
| | - Dewei Yang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China, 350018
| | - Wenyue Su
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, 361102
| | - Liuyin Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, 361102
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, 361102
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian, China, 361005
| | - Xinfu Ye
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China, 350018
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, China, 361005
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China, 361102
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China, 350018
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766, USA
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Benegiamo G, Brown SA, Panda S. RNA Dynamics in the Control of Circadian Rhythm. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:107-22. [PMID: 27256384 DOI: 10.1007/978-3-319-29073-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The circadian oscillator is based on transcription-translation feedback loops that generate 24 h oscillations in gene expression. Although circadian regulation of mRNA expression at the transcriptional level is one of the most important steps for the generation of circadian rhythms within the cell, multiple lines of evidence point to a disconnect between transcript oscillation and protein oscillation. This can be explained by regulatory RNA-binding proteins acting on the nascent transcripts to modulate their processing, export, translation and degradation rates. In this chapter we will review what is known about the different steps involved in circadian gene expression from transcription initiation to mRNA stability and translation efficiency. The role of ribonucleoprotein particles in the generation of rhythmic gene expression is only starting to be elucidated, but it is likely that they cooperate with the basal transcriptional machinery to help to maintain the precision of the clock under diverse cellular and environmental conditions.
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Affiliation(s)
- Giorgia Benegiamo
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland.,Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | - Satchidananda Panda
- Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA, 92037, USA.
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Fray RG, Simpson GG. The Arabidopsis epitranscriptome. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:17-21. [PMID: 26048078 DOI: 10.1016/j.pbi.2015.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
The most prevalent internal modification of plant messenger RNAs, N(6)-methyladenosine (m(6)A), was first discovered in the 1970s, then largely forgotten. However, the impact of modifications to eukaryote mRNA, collectively known as the epitranscriptome, has recently attracted renewed attention. mRNA methylation is required for normal Arabidopsis development and the first methylation maps reveal that thousands of Arabidopsis mRNAs are methylated. Arabidopsis is likely to be a model of wide utility in understanding the biological impacts of the epitranscriptome. We review recent progress and look ahead with questions awaiting answers to reveal an entire layer of gene regulation that has until recently been overlooked.
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Affiliation(s)
- Rupert G Fray
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK.
| | - Gordon G Simpson
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Cell and Molecular Sciences, James Hutton Institute, Invergowrie DD2 5DA, Scotland, UK.
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Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana. PLoS Genet 2015; 11:e1005474. [PMID: 26305463 PMCID: PMC4549238 DOI: 10.1371/journal.pgen.1005474] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/28/2015] [Indexed: 11/29/2022] Open
Abstract
The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. The poly(A) tail of eukaryotic mRNAs promotes export from the nucleus, translation in the cytoplasm and stability of the mRNA, and changes in poly(A)-tail length can strongly impact on gene expression. The Arabidopsis thaliana genome encodes three nuclear canonical poly(A) polymerases (PAPS1, PAPS2, PAPS4) that fulfill different functions, presumably by preferentially polyadenylating certain subpopulations of pre-mRNAs. Here, we use a fractionation-based technique to assess the transcriptome-wide impact of reduced PAPS1 activity and identify functional classes of transcripts that are particularly sensitive to reduced PAPS1 activity. Analysis of these transcripts identifies two novel biological functions for PAPS1 in ribosome biogenesis and in redox homeostasis that we confirm experimentally. By overlaying our results with information about genome-wide co-expression, we demonstrate that genes co-expressed with PAPS1 are the most strongly affected in terms of poly(A)-tail length and total-abundance changes in the paps1 mutants. This provides strong evidence that the co-expression of these genes with PAPS1 that is seen across thousands of microarrays is at least partly caused by altered activity of the PAPS1 isoform, suggesting that the plant indeed uses modulation of the balance of isoform activities to coordinately regulate the expression of groups of genes.
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